Admittedly, this is a difficult situation, and I'm not sure there are any easy answers.
I guess the first hard truth that many people learn, is that just because you deeply love someone, that doesn't mean you can necessarily always live with them. This requires a great deal caring, cooperation and compromise on both parts. A good deal of the latter, to be sure.
Secondly, you can't truly make anyone do anything, they don't really want to do. Least not apologize. And it sounds like she's really not ready to do that. The only thing you can do is give her her time and space, though do let her know that you're there if she needs you. She may come around in time, she may not.
After you give her some time apart, I guess the best approach would be to appeal to her from your child's perspective. She cared for you enough at one time to bring a life into the world with you, and that child deserves the same sort of chance that you gave your relationship. He deserves both parents in his life, and not just on weekend visitations. Try as she might to push you out of her life, for whatever obscure reason she might have, your child will always be a continual reminder of what you once shared. She might as well, at least try to make the best of what you both have, together.
Whatever you do, try to be patient with her.
I wish you luck. Take care.